A useful way of classifying phylogenetic tree visualization software is according to the size of the trees they are able to handle. I would define three main categories:
Visualising small phylogenetic trees - 2D euclidean space
The majority of tree visualization tools fall within this category. Some of the most used tools are:
These tools lay out the trees in a 2D euclidean space and are successful at visualising trees of up to a few hundred nodes. However, with more than a few hundred nodes, it is no longer possible to visualise the whole tree on one screen without increasing the level of clutter to the point where the display is unreadable. It is possible to focus in on one area of the tree, but the user then looses a sense of the context since the parts of the tree that are not in focus disappear off screen. However, although these tree visualisation tools are only able to handle a limited number of nodes, they are able to display trees with rich information content (branch lengths, bootstrap values, etc).
Visualising large phylogenetic trees - 2D hyperbolic space
Some software tools aimed at visualising large trees exploit the properties of 2D hyperbolic space to provide a focus+context view i.e. the possibility to zoom in on a particular subset of data while keeping the broader picture in view:
In hyperbolic space (as opposed to euclidean space), circumference and area increase exponentially instead of geometrically. Thus, there is enough room to allocate the same amount of space to every node, regardless of the size of the tree. Although hyperbolic space is infinite, it can be projected into a finite volume of euclidean space for a focus+context view. The result of the projection is a disc where points within the disc are magnified according to their radial distance from the center with the amount of magnification decreasing continuously and at an accelerating rate from the center to the boundary. By bringing different parts of a tree to the magnified central region, the user can examine every part of the tree in detail while retaining a sense of the context.
Visualising huge phylogenetic trees - 3D hyperbolic space
By visualising in 3D rather than 2D hyperbolic space so that the trees are rendered inside a sphere rather than a disc and by using specifically developed layout algorithms, some tools are able to interactively visualise trees with several hundred thousand nodes:
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|Last Updated ( Tuesday, 24 April 2007 )|